Mutagenetix > Incidental Mutation

Incidental Mutation 'R7261:Gpcpd1'

564602

Institutional Source

Beutler Lab

Gene Symbol

Gpcpd1

Ensembl Gene

ENSMUSG00000027346

Gene Name

glycerophosphocholine phosphodiesterase 1

Synonyms

Prei4, 2310004G06Rik, 2310032D16Rik

MMRRC Submission

045387-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.936) question?

Stock #

R7261 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

132371002-132420173 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to C at 132410619 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Cysteine to Glycine at position 23 (C23G)

Ref Sequence

ENSEMBL: ENSMUSP00000062221 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000028822] [ENSMUST00000060955] [ENSMUST00000110135] [ENSMUST00000110136] [ENSMUST00000110142] [ENSMUST00000124107] [ENSMUST00000145694] [ENSMUST00000148833] [ENSMUST00000149854]

AlphaFold

Q8C0L9

Predicted Effect

probably benign
Transcript: ENSMUST00000028822

SMART Domains

Protein: ENSMUSP00000028822
Gene: ENSMUSG00000027346

Domain	Start	End	E-Value	Type
Pfam:GDPD	142	432	1.3e-61	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000060955
AA Change: C23G

PolyPhen 2 Score 0.972 (Sensitivity: 0.77; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000062221
Gene: ENSMUSG00000027346
AA Change: C23G

Domain	Start	End	E-Value	Type
CBM_2	3	110	3.78e-29	SMART
low complexity region	142	160	N/A	INTRINSIC
low complexity region	167	175	N/A	INTRINSIC
Pfam:GDPD	326	615	5.3e-61	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000110135
AA Change: C23G

PolyPhen 2 Score 0.972 (Sensitivity: 0.77; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000105762
Gene: ENSMUSG00000027346
AA Change: C23G

Domain	Start	End	E-Value	Type
CBM_2	3	110	3.78e-29	SMART
low complexity region	146	155	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000110136

SMART Domains

Protein: ENSMUSP00000105763
Gene: ENSMUSG00000027346

Domain	Start	End	E-Value	Type
Pfam:GDPD	142	431	4.1e-59	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000110142
AA Change: C23G

PolyPhen 2 Score 0.972 (Sensitivity: 0.77; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000105769
Gene: ENSMUSG00000027346
AA Change: C23G

Domain	Start	End	E-Value	Type
CBM_2	3	110	3.78e-29	SMART
low complexity region	142	160	N/A	INTRINSIC
low complexity region	167	175	N/A	INTRINSIC
Pfam:GDPD	326	615	6.1e-63	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000124107
AA Change: C23G

PolyPhen 2 Score 0.972 (Sensitivity: 0.77; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000122751
Gene: ENSMUSG00000027346
AA Change: C23G

Domain	Start	End	E-Value	Type
CBM_2	3	110	3.78e-29	SMART
low complexity region	142	160	N/A	INTRINSIC
low complexity region	167	175	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000145694
AA Change: C23G

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000116457
Gene: ENSMUSG00000027346
AA Change: C23G

Domain	Start	End	E-Value	Type
CBM_2	3	110	3.78e-29	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000148833
AA Change: C23G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000116156
Gene: ENSMUSG00000027346
AA Change: C23G

Domain	Start	End	E-Value	Type
CBM_2	3	99	1.02e-11	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000149854
AA Change: C23G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000116949
Gene: ENSMUSG00000027346
AA Change: C23G

Domain	Start	End	E-Value	Type
CBM_2	3	94	5.54e-13	SMART

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.5%

Validation Efficiency

99% (84/85)

Allele List at MGI

Other mutations in this stock

Total: 82 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acaca	T	C	11: 84,259,526 (GRCm39)	F1954L	probably damaging	Het
Acmsd	T	G	1: 127,687,561 (GRCm39)	I281R	probably damaging	Het
Adamts2	A	T	11: 50,677,424 (GRCm39)	M742L	possibly damaging	Het
Adgrf4	G	A	17: 42,978,326 (GRCm39)	T339I	probably benign	Het
Aff1	T	C	5: 103,976,245 (GRCm39)	S448P	probably damaging	Het
Agbl2	A	T	2: 90,619,288 (GRCm39)	S38C	possibly damaging	Het
Akap7	C	T	10: 25,147,416 (GRCm39)	D105N	possibly damaging	Het
Arhgap21	A	G	2: 20,885,177 (GRCm39)	F677L	probably benign	Het
Atf6b	G	T	17: 34,869,792 (GRCm39)	V271F	probably damaging	Het
B3gnt5	A	G	16: 19,588,123 (GRCm39)	Y114C	probably damaging	Het
Casp7	T	A	19: 56,424,765 (GRCm39)	D161E	probably benign	Het
Catsper4	TTCTC	TTC	4: 133,954,423 (GRCm39)		probably null	Het
Ccdc162	T	C	10: 41,437,136 (GRCm39)	T1758A	probably benign	Het
Cfap74	C	A	4: 155,549,831 (GRCm39)	P155T	unknown	Het
Champ1	A	G	8: 13,928,517 (GRCm39)	D225G	possibly damaging	Het
Chrng	A	T	1: 87,134,962 (GRCm39)		probably null	Het
Cnksr1	T	C	4: 133,963,084 (GRCm39)		probably null	Het
Col15a1	G	A	4: 47,269,088 (GRCm39)	G582D	probably benign	Het
Cwc25	A	G	11: 97,648,585 (GRCm39)	V81A	possibly damaging	Het
Ddhd1	A	G	14: 45,894,688 (GRCm39)	Y261H	probably damaging	Het
Defa29	A	G	8: 21,816,818 (GRCm39)		probably null	Het
Diaph3	A	C	14: 87,202,893 (GRCm39)	C666G	probably benign	Het
Dlx2	A	G	2: 71,375,019 (GRCm39)	Y282H	probably damaging	Het
Dsc3	A	T	18: 20,113,814 (GRCm39)	Y369*	probably null	Het
Dtwd1	A	G	2: 126,000,424 (GRCm39)	N120S	probably benign	Het
Dysf	G	A	6: 84,169,992 (GRCm39)	S1761N	probably damaging	Het
Enthd1	A	T	15: 80,444,416 (GRCm39)	N46K	probably damaging	Het
Epha7	T	A	4: 28,813,418 (GRCm39)	I12N	probably benign	Het
Fam171a2	T	A	11: 102,328,900 (GRCm39)	N620Y	probably damaging	Het
Garin4	T	C	1: 190,896,308 (GRCm39)	S112G	unknown	Het
Gfpt2	A	T	11: 49,714,078 (GRCm39)	E278D	possibly damaging	Het
Gm3285	A	G	10: 77,698,244 (GRCm39)	Q131R	unknown	Het
Gtpbp4	A	T	13: 9,037,954 (GRCm39)	H228Q	probably benign	Het
Hdac7	A	G	15: 97,704,415 (GRCm39)	V500A	probably benign	Het
Hykk	T	G	9: 54,828,010 (GRCm39)	M83R	possibly damaging	Het
Idi1	A	G	13: 8,936,931 (GRCm39)	I101V	probably benign	Het
Irs2	A	T	8: 11,057,018 (GRCm39)	H471Q	possibly damaging	Het
Itsn1	T	C	16: 91,702,194 (GRCm39)	V12A	probably benign	Het
Jak2	A	G	19: 29,288,385 (GRCm39)	I1079V	possibly damaging	Het
Kcnt2	G	A	1: 140,282,255 (GRCm39)	R80H	possibly damaging	Het
Lamb2	T	C	9: 108,358,496 (GRCm39)	Y178H	probably damaging	Het
Lgr5	A	T	10: 115,423,370 (GRCm39)	L10Q	possibly damaging	Het
Lnx1	G	T	5: 74,838,175 (GRCm39)	S29*	probably null	Het
Lpcat3	T	A	6: 124,675,050 (GRCm39)	F57I	probably benign	Het
Manf	T	C	9: 106,769,088 (GRCm39)	T4A	probably benign	Het
Map2k3	G	A	11: 60,836,393 (GRCm39)		probably null	Het
Myh14	G	A	7: 44,273,761 (GRCm39)	Q1329*	probably null	Het
Myocd	T	C	11: 65,078,422 (GRCm39)	S458G	probably damaging	Het
Ncor2	T	C	5: 125,187,143 (GRCm39)		probably null	Het
Ndufs8	A	T	19: 3,961,606 (GRCm39)	N23K	probably benign	Het
Nkx6-1	T	C	5: 101,812,006 (GRCm39)	K32R	unknown	Het
Nlrp3	T	G	11: 59,439,272 (GRCm39)	V283G	possibly damaging	Het
Nme3	A	G	17: 25,116,037 (GRCm39)		probably null	Het
Or1o3	A	G	17: 37,574,076 (GRCm39)	F160L	probably benign	Het
Or8g23	C	T	9: 38,971,504 (GRCm39)	V153M	possibly damaging	Het
Parvg	T	C	15: 84,215,297 (GRCm39)		probably null	Het
Peg10	T	A	6: 4,756,591 (GRCm39)	M389K	unknown	Het
Phf23	G	T	11: 69,890,091 (GRCm39)	C340F	possibly damaging	Het
Piwil2	A	G	14: 70,611,860 (GRCm39)	Y929H	probably damaging	Het
Prss39	A	G	1: 34,539,369 (GRCm39)	D203G	probably damaging	Het
Prss54	G	T	8: 96,286,367 (GRCm39)	D235E	probably benign	Het
Prtg	T	A	9: 72,815,117 (GRCm39)	M1015K	possibly damaging	Het
Rbbp8	T	C	18: 11,838,799 (GRCm39)	I160T	probably damaging	Het
Rxylt1	A	T	10: 121,924,822 (GRCm39)	D293E	probably benign	Het
Scn10a	C	A	9: 119,438,790 (GRCm39)	C1692F	probably damaging	Het
Scn11a	C	T	9: 119,648,899 (GRCm39)	D55N	probably damaging	Het
Secisbp2	G	T	13: 51,836,498 (GRCm39)	V768F	probably damaging	Het
Skic3	A	G	13: 76,261,698 (GRCm39)	T138A	probably benign	Het
Spag16	T	C	1: 70,338,780 (GRCm39)	I426T	possibly damaging	Het
Sspo	G	A	6: 48,427,011 (GRCm39)	V250M	possibly damaging	Het
Strbp	A	T	2: 37,531,149 (GRCm39)		probably null	Het
Sv2c	C	T	13: 96,224,809 (GRCm39)	V167M	probably damaging	Het
Tdpoz1	G	A	3: 93,577,794 (GRCm39)	S330L	not run	Het
Tigd2	T	A	6: 59,188,052 (GRCm39)	D306E	probably benign	Het
Trrap	C	T	5: 144,782,287 (GRCm39)	P3278S	possibly damaging	Het
Vdac1	A	T	11: 52,265,761 (GRCm39)	K28N	probably damaging	Het
Vmn1r84	A	T	7: 12,096,069 (GRCm39)	M208K	probably damaging	Het
Vmn2r77	A	T	7: 86,460,518 (GRCm39)	K615*	probably null	Het
Vps11	A	G	9: 44,265,800 (GRCm39)	L493P	probably damaging	Het
Zbtb21	T	C	16: 97,754,179 (GRCm39)	I35V	possibly damaging	Het
Zbtb26	A	T	2: 37,326,667 (GRCm39)	M123K	possibly damaging	Het
Zfp236	A	T	18: 82,627,470 (GRCm39)	D1576E	possibly damaging	Het

Other mutations in Gpcpd1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00542:Gpcpd1	APN	2	132,398,903 (GRCm39)	splice site	probably null
IGL00672:Gpcpd1	APN	2	132,372,468 (GRCm39)	utr 3 prime	probably benign
IGL00676:Gpcpd1	APN	2	132,395,931 (GRCm39)	missense	probably damaging	1.00
IGL00832:Gpcpd1	APN	2	132,388,770 (GRCm39)	missense	probably damaging	1.00
IGL00931:Gpcpd1	APN	2	132,380,038 (GRCm39)	missense	probably benign	0.00
IGL01309:Gpcpd1	APN	2	132,392,244 (GRCm39)	missense	probably damaging	0.97
IGL01960:Gpcpd1	APN	2	132,381,818 (GRCm39)	critical splice donor site	probably null
IGL02110:Gpcpd1	APN	2	132,372,530 (GRCm39)	nonsense	probably null
IGL02267:Gpcpd1	APN	2	132,410,630 (GRCm39)	missense	probably damaging	1.00
IGL02570:Gpcpd1	APN	2	132,389,605 (GRCm39)	missense	probably benign	0.01
IGL02588:Gpcpd1	APN	2	132,376,673 (GRCm39)	missense	probably damaging	1.00
IGL03306:Gpcpd1	APN	2	132,375,993 (GRCm39)	critical splice donor site	probably null
Baependi	UTSW	2	132,386,355 (GRCm39)	missense	probably damaging	1.00
R0413:Gpcpd1	UTSW	2	132,406,543 (GRCm39)	splice site	probably benign
R1876:Gpcpd1	UTSW	2	132,376,673 (GRCm39)	missense	probably damaging	1.00
R4276:Gpcpd1	UTSW	2	132,382,207 (GRCm39)	missense	probably damaging	0.99
R4571:Gpcpd1	UTSW	2	132,392,270 (GRCm39)	missense	probably benign	0.05
R4849:Gpcpd1	UTSW	2	132,376,019 (GRCm39)	missense	probably damaging	1.00
R4930:Gpcpd1	UTSW	2	132,388,794 (GRCm39)	missense	probably damaging	1.00
R5060:Gpcpd1	UTSW	2	132,386,355 (GRCm39)	missense	probably damaging	1.00
R5081:Gpcpd1	UTSW	2	132,389,622 (GRCm39)	missense	probably benign	0.17
R5148:Gpcpd1	UTSW	2	132,376,110 (GRCm39)	nonsense	probably null
R5189:Gpcpd1	UTSW	2	132,395,892 (GRCm39)	missense	probably damaging	1.00
R5344:Gpcpd1	UTSW	2	132,400,597 (GRCm39)	intron	probably benign
R5623:Gpcpd1	UTSW	2	132,376,637 (GRCm39)	missense	probably damaging	1.00
R6086:Gpcpd1	UTSW	2	132,380,034 (GRCm39)	missense	probably damaging	1.00
R6787:Gpcpd1	UTSW	2	132,379,758 (GRCm39)	intron	probably benign
R6885:Gpcpd1	UTSW	2	132,395,994 (GRCm39)	missense	possibly damaging	0.56
R7223:Gpcpd1	UTSW	2	132,375,976 (GRCm39)	missense	probably benign	0.00
R7900:Gpcpd1	UTSW	2	132,376,659 (GRCm39)	missense	probably damaging	0.99
R8120:Gpcpd1	UTSW	2	132,395,943 (GRCm39)	missense	probably damaging	1.00
R8494:Gpcpd1	UTSW	2	132,386,355 (GRCm39)	missense	probably damaging	0.97
R9594:Gpcpd1	UTSW	2	132,388,848 (GRCm39)	missense	possibly damaging	0.80
X0018:Gpcpd1	UTSW	2	132,376,689 (GRCm39)	missense	probably damaging	1.00
X0060:Gpcpd1	UTSW	2	132,376,701 (GRCm39)	missense	probably damaging	1.00
X0066:Gpcpd1	UTSW	2	132,386,315 (GRCm39)	missense	probably benign	0.33

Predicted Primers

PCR Primer
(F):5'- AACCTCCCTGCCCTATGAAG -3'
(R):5'- TGGGAGTCAAGTCTTGCCTG -3'

Sequencing Primer
(F):5'- CAGATTTCTAAGTTCGAGGCCAGC -3'
(R):5'- GCCTGAGGCTCTTCTCCTC -3'

Posted On

2019-06-26